The course is organized over an 8-week period during the first semester. It is based on active learning which includes reverse approaches and problem-based activities. The time spent in class is dedicated to interactive sessions with teachers, conferences from experts in given fields, debates, methodological trainings and tutorials. Students will also be invited to provide working reports on individual or group projects elaborated autonomously before classes. Learning sequences are elaborated over the study of research articles recently published in international peer-reviewed journals. It is a question-based process the goal of which is to highlight unknown theoretical or practical contents, and to acquire what is needed to fully appreciate the information presented in the articles. The expected learning outcomes of the course are profiled in advanced and their completion monitored throughout time.

The course addresses key concepts and challenges in the following basic fields of Life Sciences and Health (LSH): Genetics/Genomics, Cellular Biology, Biochemistry and Cell Signaling. It aims to instill a solid and broad-based background while developing the student's ability to manage data, integrate/share scientific information, express their ideas and formulate questions/hypothesis whether verbally or in writing with clarity and logic.
Completion of the course is a prerequisite to enter a wide-range of M2 programs offered by the LSH's Master-Université Paris-Saclay.
Expected outcomes
Students will be able to:
-demonstrate a good understanding of fundamental facts, concepts and challenges in prominent areas of LSH
-master scientific methods and experimental procedures commonly used in LSH
-perform thorough and objective data analyses and formulate hypotheses reflecting the results
-handle informatics tools commonly used to process biological data
-handle diverse information sources and integrate/share scientific information through appropriate means
-show competence in personal and team working skills
-develop transversal skills (autonomy, adaptability, problem solving).

A bachelor's degree corresponding to a 'Licence' in France (L-M-D European system, 180 ECTS, 3-year program) or equivalent academic qualification in Science (with a Biology content) from an internationally-recognized University is required. English language proficiency equivalent to the COE/ALTE English course B2 level is required (IELTS: ?6.0, TOEFL Paper Based: ?567, TOEFL Internet: ?87, TOEIC: ?785) M1-International track M0 initial training (highly recommended).

A specific bibliography will be provided during the course.

ORSAY

Odile.bronchain@universite-paris-saclay.fr, Laurent.theodore@universite-paris-saclay.fr, Francois.AGNES@cnrs.fr.

The course is organized over an 8-week period during the first semester and runs alongside the Core courses: genes, proteins and cells. It is based on interactive learning and group work activities.

The transdisciplinary project aims to produce new knowledge or insight transcending disciplinary boundaries. The different disciplinary fields covered in this teaching unit include those of the common learning base (Core courses : Genes, proteins and cells):
-Biochemistry
-Cell signaling
-Cellular Biology
-Genomics/Genetics/Epigenetics
The transdisciplinary project aims to bring rigor, care and imagination in a collaborative production of knowledge through a project-based approach.
Expected outcomes:
• Synthesize, update and transfer scientific knowledge
• Refine understanding through discussion and explanation
• Give and receive feedback on performance
• Use of communication tools (mediatization of knowledge)
• Popularize general concepts (dissemination of knowledge)
• Develop skills specific to collaborative efforts (sharing perspectives, taking responsibilities, delegate roles motivate and help one another.

None.

September to November.

ORSAY

Pr. Bruno Colombo Pr. Christine Baldeschi Dr. Hind Guenou.

Teaching distribution 1-Part related to Cancer 3 hours of Lectures and 3 hours of Tutorials 2- Stem Cell Technology and Regenerative Medicine: 5 hours of lectures, 2 hours of tutorials and 12 hours of practical work 25 hours

Evaluation Session 1: F 1/3 CC + 2/3 EE & Session 2: F EE or EO CCcontinuous monitoring ; EEwritten exam; EOoral exam.

Teaching content :
1- CANCER
I. Introduction to gene and cell therapies
II. Gene therapy:
A. Objectives and applications
B. Tools for gene transfer: introduction to viral and non-viral vectors
C. The approaches of the anti-cancer gene therapy
III. Cell therapy:
A. Objectives and applications: immunotherapies
B. The approaches in anticancer immunotherapies
2- STEM CELL TECHNOLOGY AND REGENERATIVE MEDICINE
I. From stem cells to tissue and organ bioengineering
A.Sources of stem cell
B.Scaffolds
C.Artificial tissue and Organoids
II. Applications of stem cells to regenerative medicine.
A.Definition and characteristics of pluripotent stem cells (PSC)
B.Differentiation of PSC into epidermal cells
C.Implementation of epidermis cell therapy approach from PSC
Practical Work: Osteogenic and adipogenic differentiation of mesenchymal stem cell in vitro.
Expected outcomes :
After the course the students will be able to:
- Describe the immunotherapy or gene therapy or cell therapy in cancer
- Describe the applications of stem cells and scaffolds in tissue engineering
- Develop good laboratory practices for cells culture
- Read scientific articles and critically discuss results and conclusions.
- Demonstrate concision and precision in scientific writing.

Requires initial training in Immunology and cell biology.

Books of immunology and cell biology (e.g. Janis Kuby, Ivan Roitt, David Male, Charles Janeway) to deepen the fundamentals. Scientific articles (e.g. international newspapers referenced in Pubmed, including Medecine/Science) to follow the news of scientific advances, medical and technology.

Février - Mars - Avril.

EVRY

Pr Sylvain FISSON Dr Odile BRONCHAIN.

From the first days of the start of the academic year, the "Masteriales" will take place over 48 consecutive hours during which students will be divided into teams (e.g. quadrinomes). At the end of these two days, an oral presentation of the project and some concrete achievements will have to be made in front of a multidisciplinary teaching team and possibly an assembly of scientists, representatives of the private sector, specialists in communication and financiers. Students will be required to complete a research tender dossier (eg simplified research grant format) which will be sent one week later to the head of the unit.

Modality of the control of the knowledge (MCC): - 1st session part in the form of an oral exam (EO) and written exam (EE) - 2nd session semester in the form of a written exam (EE) and/or oral exam (EO)

Calculation of the final grades (F): - 1st session: F 1/2 EO + 1/2 EE - 2nd session: F EO and/or EE.

The concept of "Masteriales" aims to have students in small groups design an innovative thematic and/or technological research project in a limited time (48h) and to present it in an argumentative manner in front of a jury of academic and private scientists. At the end of their presentations, students must respond to a call for research (eg, simplified ANR type). Taking place from the first days of the start of the academic year, this annual edition of "Masteriales" allows a better group cohesion, a possible disinhibition and a confidence-building of the students. They also discover some of the difficulties inherent in designing research projects.

At the end of this course, students will be able to:
a) to define an innovative scientific project
b) manage teamwork and divide tasks
c) to synthesize information for oral and written restitution
d) to present clearly and forcefully a team project
e) complete a research funding application.

Upstream of this course, the students will have acquired in License (L1, L2, L3), the fundamental bases of cell biology, physiology, biochemistry and/or bioinformatics.

Scientific articles (e.g. international journals referenced in Pubmed) to draw inspiration from current scientific, medical and technological advances.

Septembre.

Claire Lurin, Etienne Delannoy, Véronique Brunaud, Marie-Laure Martin Magniette, Jean Bigeard, Florence Gonnet.

Course Objectives:
Integrative approaches are key steps in the thorough exploitation of omics data and their translation into knowledge. In this module, students will have courses on the architecture and the machinery of the cell, and on the genome and epigenome organization. They will learn how to combine predictive and experimental approaches to decode the genomic information through the structural and functional annotation of genomes. The integration and the querying of heterogeneous data imply to perfectly know their origin in order to take into consideration their quality, relevance and confidence levels. The understanding of this approach is the basis of holistic analyses for systems biology. Students will see different methods to produce transcriptome, ORFeome, proteome and interactome resources and how to integrate them in modeling approaches to have new insights on cellular processes.

On completion of the course students should be able to :
The students should have a good understanding of the challenges posed by integration of omics data. They should be able to understand and summarize a scientific paper in the field.

Novembre.

EVRY

Oliver Nüsse (UPSay) Sylvie Granon (UPSay) Hermann van Tilbeurgh (UPSay) Mohammed Taouis (UPSay) José Luis Vazquez Ibar (CEA) Jean Marie Frachisse (UPSay) Csilla Ducroq (UPSay) Heather McLean (UPSay).

The course (50h) will begin with formal English classes (8h) which will provide students with written and oral skills for constructing and presenting a short, collaborative research proposal. The proposal will be based on one of the topics developed during the series of seminars delivered by invited speakers (16h). Each collaborative proposal will be peer-evaluated by designated reviewers who will lead the discussion period following oral presentation of the project during the directed study sessions (approximately 16h). The remaining course time will be dedicated to preparing the written proposal and the oral presentation.

OAV1
Analyse, interpret and mobilize certain concepts in biology through active participation in group discussions on diverse themes including, second messenger systems, cell-cell communication, behaviour …

OAV2
Show proof of problem solving ability, creativity, critical thinking, a capacity for team work and scientific writing skills through the conception and redaction of a collaborative research project
Describe the state of the art, identify the scientific question(s), conceive experimental paradigms, predict experimental outcomes and justify their importance to the field

OAV3
Deploy public speaking skills, perfected or acquired during the course, in a formal presentation of a research project
Expose and defend a collaborative research project employing presentation skills (optimised slide content, correct phraseology, sign-posting, directive argumentation)

OAV4
Evaluate, criticize and justify scientific arguments
Organize and lead discussions on research projects written and orally presented by peers.

Given that the teaching unit is entirely in English, students are required to attest to a B2 level to participate. Placement tests will be conducted by the language department in early September.

Course material will be distributed to students before the start of the teaching unit by way of the e-campus platform.

Janvier.

ORSAY

Yacir Benomar, MCU, Emmanuel Culetto, MCU Micaela Galante, MCU Sylvie Granon, PU Jean-René Martin, DR CNRS Heather McLean, MCU Roseline Poirier, MCU.

L'UE est composée par 10 séances de TP (durée totale : 40h), chacune associée à 1hTD (durée totale TD : 10h. Une partie des TP comprend des expériences de psychophysiologie chez l'homme (sensibilité olfactive et posture), comportement chez le rongeur (anxiété et mémoire spatiale), le nématode (locomotion et olfaction) et la Drosophile (locomotion). D'autres TP sont consacrés à l'identification de structures cérébrales (souris), à l'enregistrement de l'activité électrique par électroencéphalogramme (homme), à l'étude de la signalisation de l'insuline par Western blot (souris) et à l'enregistrement de l'activité neuronale par la technique du patch clamp (souris). La rédaction de comptes-rendus approfondis sur certains des thèmes abordés en TP est requise.

OAV1. Décrire certaines des méthodologies multi-échelle utilisées en Neurosciences : des aspects comportementaux jusqu'à l'analyse cellulaire et moléculaire.
Être capable d'expliquer les approches expérimentales utilisées en Neurosciences : analyse comportementale, électrophysiologie, biologie cellulaire et moléculaire, appliquées à différents modèles vertébrés et non-vertébrés.
OAV2. Concevoir et réaliser en autonomie une démarche expérimentale.
Être capable de concevoir des protocoles expérimentaux conduisant à la production de résultats scientifiques cohérents, reproductibles, et de les analyser en autonomie.
OAV3. Intégrer les connaissances acquises en Neurosciences à travers de l'observation, la mesure et la réalisation d'expérimentations sous forme de travaux pratiques.
OAV4. Employer son esprit critique et développer sa capacité de synthèse vis-à-vis des résultats expérimentaux acquis et de la littérature scientifique. Développer ses capacités de communication scientifique écrite et orale.

Conseillé mais pas indispensable : avoir des notions de neurobiologie cellulaire et de neurobiologie du comportement.

-Electrophysiologie Moléculaire, M. Joffre, Hermann éditeurs des sciences et des arts. -Neurosciences : A la découverte du cerveau. Bear, Connors, Paradiso. Editions Pradel.

Janvier.

ORSAY

Morgane Locker Odile Bronchain Emmanuel Culetto Christophe Lefebvre Anne-Marie Pret Isabelle Guénal Marianne Malartre François Agnès.

This 5 ECTS version is constituted of two one-week internships, each in a different lab on a different organism. In some cases, a single 2 weeks project in one lab may be offered.

Working on multicellular whole organisms is often hard to realize in the environment of a classical Lab course. This workshop, in the context of a research lab on campus, is meant to allow you to address biological issues in adults or embryos, in a normal or pathological context, using the specific approaches that apply to xenopus, zebrafish, nematode, mouse, drosophila, podospora and arabidopsis.
This course will allow you to get more familiar with sophisticated imaging approaches (3D imaging, confocal microscopy, time lapse,...), as well as genetics and DNA/RNA tools that allow tissue/cell specific and temporal modulation of gene expression.
This 5 ECTS version is constituted of two one-week internships, each in a different lab on a different organism.

None.

References are specific to the lab hosting the course. They will be sent to the students once they are registered in this course.

Novembre - Décembre - Janvier.

ORSAY - EVRY - GIF-SUR-YVETTE - MONTIGNY-LE-BRETONNEUX

Janek Hyzewicz, cours Andrea Burgo, TD.

Teaching distribution CM : 16h, TD : 9h, all : 25h

Evaluation Session 1: F 1/3 CC + 2/3 EE& Session 2: F EE CCcontinuous monitoring (contrôle continu); EEwritten exam (examen écrit).

Lectures (16h)
I. Introduction to animal transgenesis
II. Design of a transgene
III. Techniques for transgene introduction into a target animal
IV. Molecular tools for genome editing
V. Applications of transgenesis in research and agriculture
VI. How to conserve a transgenic line (example with mouse)

Tutorials (9h)
Analysis of scientific papers concerning the main course topics.

Students are expected to have a strong background in molecular biology and physiology, including animal reproduction, cell and organ functions, molecular signaling, RNA, DNA and protein structure and functions… notions of microbiology, vegetal biology and organic chemistry will be required too.

Applications of animal transgenesis in research: - Li, Zhou. Construction of luciferase reporter gene vector for human MUC5AC gene promoter and analysis of its transcriptional activity. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2010 Aug;35(8):792-9. - Kautzman et al. Xkr8 Modulates Bipolar Cell Number in the Mouse Retina. Front Neurosci. 2018 Dec 3;12:876.

Example of a technique of gene transfer in embryo: - Takahashi et al. GONAD: Genome-editing via Oviductal Nucleic Acids Delivery system: a novel microinjection independent genome engineering method in mice. Sci Rep. 2015 Jun 22;5:11406.

Example

Février - Mars - Avril - Mai.

EVRY

Emmanuelle BAUDRY Olivier LESPINET.

Overview: The course is organized over an 8-week period at a rate of one day per week. Language English Hours: 50h lecture (CM) Contacts: Pierre Capy: mailto:pierre.capy@universite-paris-saclay.fr Olivier Lespinet : mailto:olivier.lespinet@universite-paris-saclay.fr Emmanuelle Baudry : mailto:emmanuelle.baudry@universite-paris-saclay.fr.

This course offers a broad vision of Evolution by exploring 'the tree of life'. It is organised around a set of conferences given by specialists. It will be introduced by an historian of Science who will discuss the progression of scientific ideas in the field of Evolution. The course begins with the origin of life and then, large groups of organisms (eukaryotes, bacteria and archaea), as well as viruses will be presented. The conferences will also be an opportunity to address various fundamental evolutionary processes such as endosymbiosis, global changes, impact of new pandemics, etc... The boundaries of our current knowledge will be addressed.
This course is intended for all students in Biology, regardless their master's speciality, as well as for students who are at the interface between Biology and other disciplines such as Physics, Chemistry, Mathematics, Physics and Computer Sciences. The goal is to provide all Master-1 students with a general culture in Evolution. This course will also be available to PhD students depending on available places.

This course is intended for all students in Biology, regardless their master's speciality, as well as for students who are at the interface between Biology and other disciplines such as Physics, Chemistry, Mathematics, Physics and Computer Sciences. The goal is to provide all Master-1 students with a general culture in Evolution. This course will also be available to PhD students depending on available places.

All books dealing with evolution.

Février - Mars - Avril.

ORSAY

Organization: The course is based on active learning. Students will be invited to work autonomously on individual or group projects before classes, using provided training documents. The time spent in class is dedicated to interactive sessions with teachers (work presentation; debate; methodological training; tutoring activities). The course is organized into 3 periods or blocks that allow for progressive achievement of learning objectives: Block 1: Problematics and concepts in developmental biology. Block 2: Tools and methods in developmental genetics. Block 3: Exploitation of concepts and methods to explore developmental processes at different scales (tissue/organ or cellular level) and in different contexts (embryonic development, regeneration, modeling of human pathologies, evolutionary processes).

Disciplinary objectives: To integrate multi-scale approaches in the organism through developmental genetics problematics. The knowledge acquired in this course will be an asset for further studies in different M2 programs, whether or not the student chooses to pursue in the developmental biology field.

Learning outcomes: At the end of the course the student should be able to:
- Formulate central concepts and problematics in developmental biology.
- Interpret, question and criticize scientific data in the field of developmental biology.
- Identify the appropriate methodology (genetic tools & technics) required for studying developmental processes at different scales and in various model organisms.
- Autonomously read, understand and criticize developmental genetics articles.
- Identify, extract and present (by oral or writing) relevant information from articles on developmental genetics.
- Perceive the relevance of developmental biology knowledge beyond the discipline itself.

Prerequisites: No specific prerequisites in developmental Biology are required. Fundamentals of Genetics, Cell Biology, Cell Signaling and Biochemistry acquired during the core courses will be exploited in the context of the developing organism.

Bibliography: Specific articles will be provided during the course. Basic concepts of developmental genetics can be consulted in "Developmental Biology" from Scott F. Gilbert (Eleventh Edition) or in "Principles of Development" by Lewis Wolpert (Oxford University Press).

Février - Mars - Avril.

ORSAY

Sébastien Bloyer (PU UPSay), Pierre Grognet (MCU, UPSay), Fabienne Malagnac (PU UPSay), Benoit Moindrot (MCU UPSay) + invited speakers (University Paris-Saclay).

This course, will combine a series of : - Lectures (chromatin epigenetics, nuclear 3D-organization, cytoplasmic inheritance, X-chromosome inactivation…) - Tutorials (epigenomics, prions, X-chromosome inactivation, chromosome conformation capture,…) - Conferences presented in the form of lectures by researchers

The course is organized over 8 weeks (half day/week), including lectures (9 hours), tutorials (5 x 2 hours) and conferences/lectures (3 x 2 hours). During tutorials students will be divided in 2 groups, one in English one in French. Students will choose their group at the beginning of the course.

During this course, the following topics will be discussed:
- How epigenetic mechanisms impact on gene expression controls, how they structure the 3D compaction of the genome and how they can be altered in human pathologies, like cancers.
- How several layers of epigenetic mechanisms are integrated during development, using the example of X-chromosome inactivation
- How epigenetic memory is set-up during differentiation and erased (stem cells (re)programming)
- How epigenetic traits can be transmitted based on self-templating structural inheritance, using the example of prions.
- Additional examples of integrated epigenetic mechanisms, at the organism or population levels, will be presented by invited researchers. Two examples in the past years: The cast and sexual polyphenisms in honey bees and aphids; The impact of nutrition on metabolic diseases and cancers

At the end of this course, the students should be able to
(1) Name, describe and discuss the different epigenetics layers impacting on gene expression levels
(2) Analyze and interpret epigenetic and epigenomic figures
(3) Portray and detail few integrated examples of epigenetic inheritances.

L3 levels in cell biology (cellular and nuclear structure), genetics (mendelian inheritance) and molecular biology (gene regulation) are requested. In addition, notions of genomics, high-throughput sequencing methods and epigenetic mechanisms developed in the Master 1 core course should be understood and comprehended.

Books available at Paris Saclay libraries: - Epigenetics by C. David Allis, Marie-Laure Caparros, Thomas Jenuwein and Danny Reinberg - Epigenetics, Nuclear Organization and Gene Function with Implications of Epigenetic Regulation and Genetic Architecture for Human Development and Health by Lucchesi and John C.

Web links : - EpiGensSys European Network Website: http://www.epigenesys.eu/fr/ - Edith Heard's lectures at the Collège de France (in French): https://www.college-de-france.fr/site/en-edith-heard/_course.htm.

Février - Mars - Avril.

ORSAY

Marie-Anne Debily Elisabeth Petit-Teixeira Researchers of Genopole® campus and Gustave Roussy Cancer center.

The course consists in lectures, analysis of genomic studies based on several publications during tutorials and illustrations by research seminars given by Genopole® campus and Gustave Roussy Cancer center experts that will highlight the contribution of these global approaches to the understanding of cellular processes and human complex diseases. Oral presentations of scientific research will be held by the students in a seminar format during the course.

This course provides a thorough knowledge of genome-wide studies from experimental design to integrative data analysis: Explore genomic variations in both health and disease to understand gene function and regulation of expression, decipher pathogenesis mechanisms, identify therapeutic opportunities and treatments in the context of precision medicine.

-Enumerate and differentiate large-scale sequencing technology driven-approaches at different levels, i.e. genomics, transcriptomics, epigenetic landscapes.
-Determine which technology to use among a broad spectrum of functional genomics methods to address specific biological questions
-Precise the main classification methods œfor patient stratification and identification of co-regulated genes
-Interpret results of large-scale experimental datasets in a scientifically stringent manner
-Critically examine research publications dealing with functional genomics
-Understand how to identify altered signaling pathways, biological process and biomarkers from genes list by functional annotation tools,
-Specify the advantages of single-cell approaches regarding the dynamic of transcriptome, tissue complexity or polyclonal sample content.

Molecular Biology of the Cell: Alberts, Johnson, Lewis, Raff, Roberts, Walter Scientific articles and review on recent concepts and advances in Applied genomics.

Février - Mars - Avril.

EVRY

Pr Sylvain FISSON Pr Bruno COLOMBO.

Modality of the control of the knowledge (MCC): - Continuous Control (CC) during workshop sessions • Students will be divided into teams (e.g. trinomials). They will have to choose a scientific article and a review proposed by the teachers and present orally, with the help of PowerPoint support, the content of the article by explaining the relevance of the question asked and the experimental strategy implemented. • Spot checks may be conducted during the various working sessions. - 1st session semester in the form of a written examination (EE) - 2nd session semester in the form of a written exam (EE) and/or oral exam (EO)

Calculation of the final grades (F): - 1st session: F 1/3 CC + 2/3 EE - 2nd session: F EE and/or EO.

At the end of this course, students will be able to:
a) describe the components of the immune system (molecules, cells, tissues and organs) as well as the underlying mechanisms associated with its dysfunction
b) to argue about the role played by the immune system in different types of vaccination strategies, as well as during tissue transplants
c) to clarify the role of immunosurveillance of the immune system limiting the emergence of cancers
d) to analyze, interpret and describe the results presented in scientific articles

Lesson plan:
A) Lectures (CM):
1. Allergies (2h)
2. Mucosal immunity (2h)
3. Anti-infectious immunity (2h)
4. Vaccination strategies (2h)
5. Autoimmune diseases (2h)
6. Anti-tumor immunity (2h)
7. Immunodeficiencies (2h)
8. Transplantations (2h)
B) Tutorials (TD):
- Analysis of scientific articles on topics developed in the lessons.

Upstream of this course, students should have acquired the basic bases of Immunology, in particular by having followed the unit "Physiology of the Immune System" (UEVE) or another unit of fundamental immunology (M1 and/or Licence-Bachelor). In particular, students should be able to identify the main cells and molecules involved in immune responses. They should also be able to describe the main physiological mechanisms of innate and adaptive immunity.

Books on immunology and immunobiology (e.g. ASSIM books, Janis Kuby, Ivan Roitt, David Male, Charles Janeway). Recent and old scientific articles, to explain the fundamentals and the scientific advances.

Février - Mars.

EVRY

Olga Soutourina (PU UPSay) Ombeline Rossier (MCU UPSay) Johann Peltier (MCU UPSay).

Conferences: 10 hours Tutorial classes; Supervision/project tutoring 10 hours Personal work: at least 10 hours Oral examination and report.

The purpose of this teaching unit is to propose to students to explore a scientific question in Microbiology in an integrated way, both in terms of scale of analysis (from the molecule to the ecosystem) and methodologies or applications.
The students will carry out a personal project framed around a given aspect that they have chosen and that will be part of a general theme common to the whole class. Thus, collectively, the multiple facets of a current issue around an infectious agent will be taken into consideration, from the physiology and pathogenesis of the agent, to the interactions it maintains with the microbial communities and/or the host, to the practical implications of this knowledge in health or biotechnology. For example, Clostridium difficile infection may be a topic that can generate personal projects based on microbial interactions within intestinal microbiota (dysbiosis, bacteriophages), epidemiology (hypervirulent strains, recurrent infections) and therapeutic strategies. In connection with the problem addressed, students will be trained to use metagenomic data to compare the composition of the microbiota under standard conditions or following disturbances induced by antibiotic treatments and pathogen development.

Knowledge base in General Microbiology, Genetics, Molecular and Cell Biology, Biochemistry Open for Paris-Saclay International track.

Scientific papers and books in the field of Microbiology, documents on eCampus platform.

Février - Mars - Avril.

ORSAY - GIF-SUR-YVETTE

Catherine Berrier, PU Micaela Galante, MCU Sabir Jacquir, PU.

Cette UE de 25h est composée de 18h de cours et de 7h de travaux dirigés. Les séances de travaux dirigés sont vouées à résoudre des exercices basés sur des extraits de publications scientifiques et à l'analyse d'articles.

OAV1. Mettre en relation structure et fonctionnement des canaux ioniques
-Maitriser les concepts de base d'électrochimie et d'électrophysiologie nécessaires à la compréhension des propriétés électriques des membranaires.
-Expliquer les principes et les méthodes d'étude électrophysiologique des canaux ioniques.
-Relier les paramètres étudiés en électrophysiologie au mode d'action moléculaire des canaux ioniques.
OAV2. Décrire les principes de la communication intercellulaire dans le système nerveux et schématiser les étapes qui portent à la libération des neurotransmetteurs.
-Maîtriser les concepts fondamentaux de la Neuropharmacologie Moléculaire (affinité, activité et efficacité d'un médicament, courbe dose-effet, caractéristique liaison-effet, ..).
-Décrire les mécanismes de libération de neurotransmetteurs (transmission cholinergique).
OAV3. Décrire et schématiser les caractéristiques des récepteurs ionotropiques du glutamate et comparer leurs rôles à la synapse.
-Décrire la structure et caractériser les propriétés électrophysiologiques/pharmacologiques des récepteurs de type AMPA et NMDA.
-Décrire la coopération entre ces deux types de récepteurs à la synapse et leur implication dans la plasticité synaptique à long terme.

Architecture fonctionnelle et anatomique du neurone, structure de la membrane plasmique.

Physiologie du neurone, Tritsch-Chesnoy-Marchais-Felz, Ed. Doin. Biochimie et Biophysique des membranes, E. Shechter, Ed. Dunod. Cellular and Molecular Neuropharmacology, C. Hammond, Ed. Academic Press. From Molecules to networks, an introduction to Cellular and Molecular, J. H. Byrne-J. L. Roberts, Ed. Academic Press. Neurosciences, M. F. Bear-B. W. Connors-A. Paradiso, Ed. Pradel. Synapses, T. C. Südhof-C. F. Stevens, Ed. W. Maxwell CowanHoward Hughes Medical Institute.

Décembre.

ORSAY

Micaela Galante (UPSay) Emmanuel Culetto (UPSay) Valérie Enderline (UPSay) Jean-René Martin (CNRS) Sylvie Granon (UPSay) Daniel Shultz (CNRS) Isabelle Ferezou (CNRS) Heather McLean (UPSay).

L’UE est composée de cours magistraux (40h) et de travaux dirigés (10h) dispensés par des intervenants (enseignants-chercheurs et chercheurs). Les travaux dirigés sont essentiellement consacrés à l’analyse et la présentation des articles scientifiques illustrant des thèmes traités en cours. Les séances se dérouleront sous forme de présentation classique des articles ou sous forme de table ronde (travail de mise en débat de l’analyse par groupe avant une restitution collective). Un objectif majeur de ces séances est de raffiner les savoir-faire relatifs à la communication à travers des discussions collectives. Les cours magistraux et les travaux dirigés seront dispensés en français ou en anglais.

OAV1
Décrire et formaliser les fondements de la perception sensorielle
Mobiliser et restituer des connaissances sur la transduction, l’intégration et le codage de stimuli sensoriels (auditif, somesthésique, olfactif et visuel) par le système nerveux (modèles vertébrés et non-vertébrés)

OAV2
Enumérer le rôle de différents réseaux neuronaux à la base de divers comportements intégratifs
Analyser et interpréter des données expérimentales pour démontrer le rôle de certaines structures dans l’activité locomotrice et l’apprentissage moteur (cervelet)

OAV3
Illustrer et restituer des connaissances sur des mécanismes neurobiologiques, neurochimiques, cellulaires et moléculaires fondamentaux de la mémoire et la prise de décision dans des conditions normales et pathologiques

OAV4
Evaluer, critiquer et valoriser des arguments scientifiques représentant les avancées les plus récentes dans les domaines de recherche traités en cours
En s’appuyant sur les enseignements dispensés, l’étudiant sera capable d’interpréter, d’analyser et d’argumenter des articles scientifiques, afin de pouvoir animer une discussion scientifique, tout en gardant un esprit à la fois ouvert et critique.

Connaissances de neurobiologie cellulaire et de neuroanatomie fonctionnelle niveau licence 3ième année (voir bibliographie).

Les étudiants en Master 1 doivent avoir acquis en amont des connaissances basiques du système nerveux. Pour aider à la consolidation des connaissances, les livres suivants peuvent être utiles : Les bases de neurobiologie cellulaire : Physiologie du Neurone. Tritsch, Chesnoy-Marchais, Feltz. Editions Doin Les bases des systèmes sensoriels : Neurosciences : A la découverte du cerveau. Bear, Connors, Paradiso. Editions Pradel

Les articles de revue, publiés dans des journaux scientifiques réputés (et en langue anglaise) peuvent être mis à la disposition des étudiants.

Février - Mars - Avril.

ORSAY

Matthieu Jules (AgroParisTech, Micalis), Vincent Fromion (INRA, MaIAGE), Anne Goelzer (INRA, MaIAGE), Vincent Sauveplane (AgroParisTech, Micalis), Laurent Tournier (INRA, MaIAGE).

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological tools.

Global analyses (omics) currently generate large datasets that do not capture the complexity of living systems. Systems Biology is an approach where omics data are integrated and exploited (compared) through mathematical models of biological systems or sub-systems. The complexity of biological systems and the diversity of issues to be considered require the use of different types of modelling.
In this course, students will explore a number of mathematical approaches to tackle biological issues through the integration of "omics" data. The mathematical approaches include the methods known as constraint-based modeling, i.e. flux balance analysis, resource balance analysis, but also tools specific to the analysis of dynamic systems and Boolean systems.
On completion of the course students will be able to :
•understand and explain the challenges of using constraint-based modeling approaches to describe cellular behaviors
•summarize and present a scientific paper in the field.

The ability to use Matlab will be an asset but is not a prerequisite.

Recent and past scientific articles, to explain the fundamentals and scientific advances in systems biology. Two general references on these approaches : Systems Biology [Textbook], E. Klipp et al, Wiley-Blackwell, 2011. Metabolic engineering in the post genomic era, ed. B.N. Kholodenko, H.V. Westerhoff, Taylor & Francis, 2004.

Décembre.

JOUY-EN-JOSAS

Matthieu Jules Vincent Sauveplane Wolfram Liebermeister.

The course module is organized in 15h of lectures and 10h of tutorials to introduce knowledge and methodological tools.

In recent years the dynamics of biological systems has been increasingly described using concepts and terminology borrowed from economics: cells face trade-offs between different strategies for survival; metabolism can be viewed as a resource allocation problem; biomolecules can be associated with a 'value' within the free energy 'market' of the cell, etc. These concepts indicate the emergence of a new way of thinking about problems in biology.
In this course, we will explore biological questions that can be addressed using concepts of resource allocation, efficiency and optimality on (1) genome-scale cellular metabolism, (2) gene expression and protein synthesis, (3) cellular fitness and (4) game theory in cellular and multicellular biology.
At the end of the course, students will be able to:
•Explain the principles of cellular economics and resource allocation in living systems
•Analyse simple growth strategies of living systems in a competitive environment
•Describe simple models and identify their advantages and limitations.

Several first semester optional modules are highly recommended: Systems Biology I Systems Biology II.

Recent and past scientific articles, to explain the fundamentals and scientific advances in game theory, cellular resource allocation, cellular fitness, growth strategies etc. For instance, relevant publications are: •Shifts in growth strategies reflect tradeoffs in cellular economics. Molenaar D, van Berlo R, de Ridder D, Teusink B. ; Mol Syst Biol. 2009 •Mechanistic links between cellular trade-offs, gene expression, and growth. Weiße AY, Oyarzún DA, Danos V, Swain PS. ; Proc Natl Acad Sci U S A. 2015 •Plant height and evolutionary games. DS Falster and M Westoby; TRENDS in Ecology and

Décembre - Janvier.

JOUY-EN-JOSAS

Ioana Popescu Matthieu Jules Cécile Gasse.

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological tools.

The aim of this module is to give students perspectives in Synthetic Biology, a field where novel biological and biologically based parts, devices and systems are (re)designed and constructed to perform new functions that do not exist in nature.
At the end of the course, students will be able to:
- Explain the strategies employed in the field of metabolic engineering for the production of sustainable biobased compounds
- Analyse simple synthetic regulatory circuits
- Explain the principles of genome engineering techniques and illustrate the synthetic genomics approaches
- Describe several orthogonal systems and analyse their advantages and limitations
Thus, students will have a strategic vision on how to progress in the field of synthetic biology: from the extraction of innovative knowledge from the available biological data to the transformation of the data into new rational and useful knowledge.

Several first semester optional modules are highly recommended: Systems Biology I Systems Biology II Cellular Economics.

Paul S Freemont (Editor) and Richard I Kitney (Editor). Synthetic Biology: A Primer. Imperial College Press, 2012. Daniel G. Gibson (Editor), Clyde A. Hutchison (III) (Editor), Hamilton Othanel Smith (Editor) and J. Craig Venter (Editor). Synthetic Biology: Tools for Engineering Biological Systems. Cold Spring Harbor Laboratory Press, 2017. Christina Smolke (Editor), Sang Yup Lee (Series Editor), Jens Nielsen (Series Editor) and Gregory Stephanopoulos (Series Editor). Synthetic Biology: Parts, Devices and Applications. Wiley-Blackwell, 2018.

Février - Mars - Avril.

EVRY

Morgane Locker Odile Bronchain Emmanuel Culetto Christophe Lefebvre Anne-Marie Pret Isabelle Guénal Marianne Malartre François Agnès.

One week in a lab from Paris-Saclay.

Working on multicellular whole organisms is often hard to realize in the environment of a classical Lab course. This workshop, in the context of a research lab on campus, is meant to allow you to address biological issues in adults or embryos, in a normal or pathological context, using the specific approaches that apply to xenopus, zebrafish, nematode, mouse, drosophila, podospora and arabidopsis.
This course will allow you to get more familiar with sophisticated imaging approaches (3D imaging, confocal microscopy, time lapse,...), as well as genetics and DNA/RNA tools that allow tissue/cell specific and temporal modulation of gene expression.
This 2,5 ECTS version is a one-week internship.

None.

References will be sent by the tutor, depending on the subject/lab.

Novembre - Décembre - Janvier.

ORSAY - GIF-SUR-YVETTE - MONTIGNY-LE-BRETONNEUX

Responsables Université Paris-Saclay : Marie-Hélène Cuif, marie-helene.cuif@universite-paris-saclay.fr Sébastien Bloyer, sebastien.bloyer@universite-paris-saclay.fr Odile Bronchain, odile.bronchain@universite-paris-saclay.fr Cécile Lagaudrière, cecile.lagaudriere-gesbert@universite-paris-saclay.fr Sylvain Fisson, sylvain.fisson@univ-evry.fr.

During the first semester, the students have to find a host laboratory. To this end they must write a CV, consult the internship offers and contact research teams of their choice for an interview. The internship is tied up to the 'Scientific project' teaching unit, during which the scientific context and the experimental approaches suitable to address the biological questions will be defined. The internship spans 8-weeks in an academic laboratory or in a R&D department within a company, in France or abroad. At the end of the internship, the students complete a research report and an oral presentation, to highlight the biological questions raised, the experimental designs and to present and discuss their results.

The internship allows students to get familiar with various experimental approaches as well as the daily activities of a research team.
During the internship, the students participate in an ongoing research project under the guidance of laboratory staff scientists or engineers. They attend lab meetings and conferences. They are introduced to the hygiene and safety rules. They acquire and analyze experimental data. They have to synthetize their results in the form of a written report and an oral defense.
At the end of this teaching unit, the student will be able to:
- apply to research teams
- integrate a research team and participate in its activities
- follow Health and Safety rules
- to carry out a scientific experiment and integrate the controls required for its interpretation.
- write a laboratory notebook
- analyze critically the results obtained
- synthesize and present a scientific research process and the results obtained in oral and written form.

None.

Avril - Mai - Juin.

SCEAUX - ORSAY - GUYANCOURT - EVRY - GIF-SUR-YVETTE - CHATENAY - VERSAILLES - PARIS - KREMLIN-BICETRE - ST-QUENTIN-EN-YVELINES - PALAISEAU - MONTIGNY-LE-BRETONNEUX - COURCOURONNES - BURES-SUR-YVETTE - JOUY-EN-JOSAS

Responsables Université Paris-Saclay : Marie-Hélène Cuif, marie-helene.cuif@universite-paris-saclay.fr Sébastien Bloyer, sebastien.bloyer@universite-paris-saclay.fr Odile Bronchain, odile.bronchain@universite-paris-saclay.fr Cécile Lagaudrière, cecile.lagaudriere-gesbert@universite-paris-saclay.fr Sylvain Fisson, sylvain.fisson@univ-evry.fr Frédéric Crémazy, frederic.cremazy@uvsq.fr.

The Scientific Project is organized over a period of 8 weeks at a rate of one day per week spent in the host laboratory. This period is devoted to discussions between the student and his supervisor, the reflection and a bibliographic work to define the internship project. The student will present a bibliographic synthesis of the topic and the problematic of his internship project in a written report.

The Scientific Project is a groundwork for the laboratory internship. It consists of a thoughtful work based on bibliographic researches and on discussions with the internship's supervisor.
It aims at clarifying the general scientific context and the state of knowledge. It allows highlighting the scientific questions that will be addressed during the internship, the experimental models chosen and the workflow of experiences that will be conducted. The whole is synthesized in a written report.
At the end of this training, the student will be able to:
- define a biological problem
- acquire, analyze and synthesize data from the literature
- formulate scientific hypotheses
- build a coherent scientific approach
- write a research project.

None.

None.

Février - Mars - Avril.

Oliver Nüsse (UPSay) Sylvie Granon (UPSay) Hermann van Tilbeurgh (UPSay) Mohammed Taouis (UPSay) José Luis Vazquez Ibar (CEA) Jean Marie Frachisse (UPSay) Csilla Ducroq (UPSay) Heather McLean (UPSay).

The course (50h) will begin with formal English classes (8h) which will provide students with written and oral skills for constructing and presenting a short, collaborative research proposal. The proposal will be based on one of the topics developed during the series of seminars delivered by invited speakers (16h). Each collaborative proposal will be peer-evaluated by designated reviewers who will lead the discussion period following oral presentation of the project during the directed study sessions (approximately 16h). The remaining course time will be dedicated to preparing the written proposal and the oral presentation.

OAV1
Analyse, interpret and mobilize certain concepts in biology through active participation in group discussions on diverse themes including, second messenger systems, cell-cell communication, behaviour …

OAV2
Show proof of problem solving ability, creativity, critical thinking, a capacity for team work and scientific writing skills through the conception and redaction of a collaborative research project
Describe the state of the art, identify the scientific question(s), conceive experimental paradigms, predict experimental outcomes and justify their importance to the field

OAV3
Deploy public speaking skills, perfected or acquired during the course, in a formal presentation of a research project
Expose and defend a collaborative research project employing presentation skills (optimised slide content, correct phraseology, sign-posting, directive argumentation)

OAV4
Evaluate, criticize and justify scientific arguments
Organize and lead discussions on research projects written and orally presented by peers.

Given that the teaching unit is entirely in English, students are required to attest to a B2 level to participate. Placement tests will be conducted by the language department in early September.

Course material will be distributed to students before the start of the teaching unit by way of the e-campus platform.

Janvier.

ORSAY

Yacir Benomar, MCU, Emmanuel Culetto, MCU Micaela Galante, MCU Sylvie Granon, PU Jean-René Martin, DR CNRS Heather McLean, MCU Roseline Poirier, MCU.

L'UE est composée par 10 séances de TP (durée totale : 40h), chacune associée à 1hTD (durée totale TD : 10h. Une partie des TP comprend des expériences de psychophysiologie chez l'homme (sensibilité olfactive et posture), comportement chez le rongeur (anxiété et mémoire spatiale), le nématode (locomotion et olfaction) et la Drosophile (locomotion). D'autres TP sont consacrés à l'identification de structures cérébrales (souris), à l'enregistrement de l'activité électrique par électroencéphalogramme (homme), à l'étude de la signalisation de l'insuline par Western blot (souris) et à l'enregistrement de l'activité neuronale par la technique du patch clamp (souris). La rédaction de comptes-rendus approfondis sur certains des thèmes abordés en TP est requise.

OAV1. Décrire certaines des méthodologies multi-échelle utilisées en Neurosciences : des aspects comportementaux jusqu'à l'analyse cellulaire et moléculaire.
Être capable d'expliquer les approches expérimentales utilisées en Neurosciences : analyse comportementale, électrophysiologie, biologie cellulaire et moléculaire, appliquées à différents modèles vertébrés et non-vertébrés.
OAV2. Concevoir et réaliser en autonomie une démarche expérimentale.
Être capable de concevoir des protocoles expérimentaux conduisant à la production de résultats scientifiques cohérents, reproductibles, et de les analyser en autonomie.
OAV3. Intégrer les connaissances acquises en Neurosciences à travers de l'observation, la mesure et la réalisation d'expérimentations sous forme de travaux pratiques.
OAV4. Employer son esprit critique et développer sa capacité de synthèse vis-à-vis des résultats expérimentaux acquis et de la littérature scientifique. Développer ses capacités de communication scientifique écrite et orale.

Conseillé mais pas indispensable : avoir des notions de neurobiologie cellulaire et de neurobiologie du comportement.

-Electrophysiologie Moléculaire, M. Joffre, Hermann éditeurs des sciences et des arts. -Neurosciences : A la découverte du cerveau. Bear, Connors, Paradiso. Editions Pradel.

Janvier.

ORSAY

Morgane Locker Odile Bronchain Emmanuel Culetto Christophe Lefebvre Anne-Marie Pret Isabelle Guénal Marianne Malartre François Agnès.

This 5 ECTS version is constituted of two one-week internships, each in a different lab on a different organism. In some cases, a single 2 weeks project in one lab may be offered.

Working on multicellular whole organisms is often hard to realize in the environment of a classical Lab course. This workshop, in the context of a research lab on campus, is meant to allow you to address biological issues in adults or embryos, in a normal or pathological context, using the specific approaches that apply to xenopus, zebrafish, nematode, mouse, drosophila, podospora and arabidopsis.
This course will allow you to get more familiar with sophisticated imaging approaches (3D imaging, confocal microscopy, time lapse,...), as well as genetics and DNA/RNA tools that allow tissue/cell specific and temporal modulation of gene expression.
This 5 ECTS version is constituted of two one-week internships, each in a different lab on a different organism.

None.

References are specific to the lab hosting the course. They will be sent to the students once they are registered in this course.

Novembre - Décembre - Janvier.

ORSAY - EVRY - GIF-SUR-YVETTE - MONTIGNY-LE-BRETONNEUX

Janek Hyzewicz, cours Andrea Burgo, TD.

Teaching distribution CM : 16h, TD : 9h, all : 25h

Evaluation Session 1: F 1/3 CC + 2/3 EE& Session 2: F EE CCcontinuous monitoring (contrôle continu); EEwritten exam (examen écrit).

Lectures (16h)
I. Introduction to animal transgenesis
II. Design of a transgene
III. Techniques for transgene introduction into a target animal
IV. Molecular tools for genome editing
V. Applications of transgenesis in research and agriculture
VI. How to conserve a transgenic line (example with mouse)

Tutorials (9h)
Analysis of scientific papers concerning the main course topics.

Students are expected to have a strong background in molecular biology and physiology, including animal reproduction, cell and organ functions, molecular signaling, RNA, DNA and protein structure and functions… notions of microbiology, vegetal biology and organic chemistry will be required too.

Applications of animal transgenesis in research: - Li, Zhou. Construction of luciferase reporter gene vector for human MUC5AC gene promoter and analysis of its transcriptional activity. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2010 Aug;35(8):792-9. - Kautzman et al. Xkr8 Modulates Bipolar Cell Number in the Mouse Retina. Front Neurosci. 2018 Dec 3;12:876.

Example of a technique of gene transfer in embryo: - Takahashi et al. GONAD: Genome-editing via Oviductal Nucleic Acids Delivery system: a novel microinjection independent genome engineering method in mice. Sci Rep. 2015 Jun 22;5:11406.

Example

Février - Mars - Avril - Mai.

EVRY

Emmanuelle BAUDRY Olivier LESPINET.

Overview: The course is organized over an 8-week period at a rate of one day per week. Language English Hours: 50h lecture (CM) Contacts: Pierre Capy: mailto:pierre.capy@universite-paris-saclay.fr Olivier Lespinet : mailto:olivier.lespinet@universite-paris-saclay.fr Emmanuelle Baudry : mailto:emmanuelle.baudry@universite-paris-saclay.fr.

This course offers a broad vision of Evolution by exploring 'the tree of life'. It is organised around a set of conferences given by specialists. It will be introduced by an historian of Science who will discuss the progression of scientific ideas in the field of Evolution. The course begins with the origin of life and then, large groups of organisms (eukaryotes, bacteria and archaea), as well as viruses will be presented. The conferences will also be an opportunity to address various fundamental evolutionary processes such as endosymbiosis, global changes, impact of new pandemics, etc... The boundaries of our current knowledge will be addressed.
This course is intended for all students in Biology, regardless their master's speciality, as well as for students who are at the interface between Biology and other disciplines such as Physics, Chemistry, Mathematics, Physics and Computer Sciences. The goal is to provide all Master-1 students with a general culture in Evolution. This course will also be available to PhD students depending on available places.

This course is intended for all students in Biology, regardless their master's speciality, as well as for students who are at the interface between Biology and other disciplines such as Physics, Chemistry, Mathematics, Physics and Computer Sciences. The goal is to provide all Master-1 students with a general culture in Evolution. This course will also be available to PhD students depending on available places.

All books dealing with evolution.

Février - Mars - Avril.

ORSAY

Organization: The course is based on active learning. Students will be invited to work autonomously on individual or group projects before classes, using provided training documents. The time spent in class is dedicated to interactive sessions with teachers (work presentation; debate; methodological training; tutoring activities). The course is organized into 3 periods or blocks that allow for progressive achievement of learning objectives: Block 1: Problematics and concepts in developmental biology. Block 2: Tools and methods in developmental genetics. Block 3: Exploitation of concepts and methods to explore developmental processes at different scales (tissue/organ or cellular level) and in different contexts (embryonic development, regeneration, modeling of human pathologies, evolutionary processes).

Disciplinary objectives: To integrate multi-scale approaches in the organism through developmental genetics problematics. The knowledge acquired in this course will be an asset for further studies in different M2 programs, whether or not the student chooses to pursue in the developmental biology field.

Learning outcomes: At the end of the course the student should be able to:
- Formulate central concepts and problematics in developmental biology.
- Interpret, question and criticize scientific data in the field of developmental biology.
- Identify the appropriate methodology (genetic tools & technics) required for studying developmental processes at different scales and in various model organisms.
- Autonomously read, understand and criticize developmental genetics articles.
- Identify, extract and present (by oral or writing) relevant information from articles on developmental genetics.
- Perceive the relevance of developmental biology knowledge beyond the discipline itself.

Prerequisites: No specific prerequisites in developmental Biology are required. Fundamentals of Genetics, Cell Biology, Cell Signaling and Biochemistry acquired during the core courses will be exploited in the context of the developing organism.

Bibliography: Specific articles will be provided during the course. Basic concepts of developmental genetics can be consulted in "Developmental Biology" from Scott F. Gilbert (Eleventh Edition) or in "Principles of Development" by Lewis Wolpert (Oxford University Press).

Février - Mars - Avril.

ORSAY

Sébastien Bloyer (PU UPSay), Pierre Grognet (MCU, UPSay), Fabienne Malagnac (PU UPSay), Benoit Moindrot (MCU UPSay) + invited speakers (University Paris-Saclay).

This course, will combine a series of : - Lectures (chromatin epigenetics, nuclear 3D-organization, cytoplasmic inheritance, X-chromosome inactivation…) - Tutorials (epigenomics, prions, X-chromosome inactivation, chromosome conformation capture,…) - Conferences presented in the form of lectures by researchers

The course is organized over 8 weeks (half day/week), including lectures (9 hours), tutorials (5 x 2 hours) and conferences/lectures (3 x 2 hours). During tutorials students will be divided in 2 groups, one in English one in French. Students will choose their group at the beginning of the course.

During this course, the following topics will be discussed:
- How epigenetic mechanisms impact on gene expression controls, how they structure the 3D compaction of the genome and how they can be altered in human pathologies, like cancers.
- How several layers of epigenetic mechanisms are integrated during development, using the example of X-chromosome inactivation
- How epigenetic memory is set-up during differentiation and erased (stem cells (re)programming)
- How epigenetic traits can be transmitted based on self-templating structural inheritance, using the example of prions.
- Additional examples of integrated epigenetic mechanisms, at the organism or population levels, will be presented by invited researchers. Two examples in the past years: The cast and sexual polyphenisms in honey bees and aphids; The impact of nutrition on metabolic diseases and cancers

At the end of this course, the students should be able to
(1) Name, describe and discuss the different epigenetics layers impacting on gene expression levels
(2) Analyze and interpret epigenetic and epigenomic figures
(3) Portray and detail few integrated examples of epigenetic inheritances.

L3 levels in cell biology (cellular and nuclear structure), genetics (mendelian inheritance) and molecular biology (gene regulation) are requested. In addition, notions of genomics, high-throughput sequencing methods and epigenetic mechanisms developed in the Master 1 core course should be understood and comprehended.

Books available at Paris Saclay libraries: - Epigenetics by C. David Allis, Marie-Laure Caparros, Thomas Jenuwein and Danny Reinberg - Epigenetics, Nuclear Organization and Gene Function with Implications of Epigenetic Regulation and Genetic Architecture for Human Development and Health by Lucchesi and John C.

Web links : - EpiGensSys European Network Website: http://www.epigenesys.eu/fr/ - Edith Heard's lectures at the Collège de France (in French): https://www.college-de-france.fr/site/en-edith-heard/_course.htm.

Février - Mars - Avril.

ORSAY

Marie-Anne Debily Elisabeth Petit-Teixeira Researchers of Genopole® campus and Gustave Roussy Cancer center.

The course consists in lectures, analysis of genomic studies based on several publications during tutorials and illustrations by research seminars given by Genopole® campus and Gustave Roussy Cancer center experts that will highlight the contribution of these global approaches to the understanding of cellular processes and human complex diseases. Oral presentations of scientific research will be held by the students in a seminar format during the course.

This course provides a thorough knowledge of genome-wide studies from experimental design to integrative data analysis: Explore genomic variations in both health and disease to understand gene function and regulation of expression, decipher pathogenesis mechanisms, identify therapeutic opportunities and treatments in the context of precision medicine.

-Enumerate and differentiate large-scale sequencing technology driven-approaches at different levels, i.e. genomics, transcriptomics, epigenetic landscapes.
-Determine which technology to use among a broad spectrum of functional genomics methods to address specific biological questions
-Precise the main classification methods œfor patient stratification and identification of co-regulated genes
-Interpret results of large-scale experimental datasets in a scientifically stringent manner
-Critically examine research publications dealing with functional genomics
-Understand how to identify altered signaling pathways, biological process and biomarkers from genes list by functional annotation tools,
-Specify the advantages of single-cell approaches regarding the dynamic of transcriptome, tissue complexity or polyclonal sample content.

Molecular Biology of the Cell: Alberts, Johnson, Lewis, Raff, Roberts, Walter Scientific articles and review on recent concepts and advances in Applied genomics.

Février - Mars - Avril.

EVRY

Pr Sylvain FISSON Pr Bruno COLOMBO.

Modality of the control of the knowledge (MCC): - Continuous Control (CC) during workshop sessions • Students will be divided into teams (e.g. trinomials). They will have to choose a scientific article and a review proposed by the teachers and present orally, with the help of PowerPoint support, the content of the article by explaining the relevance of the question asked and the experimental strategy implemented. • Spot checks may be conducted during the various working sessions. - 1st session semester in the form of a written examination (EE) - 2nd session semester in the form of a written exam (EE) and/or oral exam (EO)

Calculation of the final grades (F): - 1st session: F 1/3 CC + 2/3 EE - 2nd session: F EE and/or EO.

At the end of this course, students will be able to:
a) describe the components of the immune system (molecules, cells, tissues and organs) as well as the underlying mechanisms associated with its dysfunction
b) to argue about the role played by the immune system in different types of vaccination strategies, as well as during tissue transplants
c) to clarify the role of immunosurveillance of the immune system limiting the emergence of cancers
d) to analyze, interpret and describe the results presented in scientific articles

Lesson plan:
A) Lectures (CM):
1. Allergies (2h)
2. Mucosal immunity (2h)
3. Anti-infectious immunity (2h)
4. Vaccination strategies (2h)
5. Autoimmune diseases (2h)
6. Anti-tumor immunity (2h)
7. Immunodeficiencies (2h)
8. Transplantations (2h)
B) Tutorials (TD):
- Analysis of scientific articles on topics developed in the lessons.

Upstream of this course, students should have acquired the basic bases of Immunology, in particular by having followed the unit "Physiology of the Immune System" (UEVE) or another unit of fundamental immunology (M1 and/or Licence-Bachelor). In particular, students should be able to identify the main cells and molecules involved in immune responses. They should also be able to describe the main physiological mechanisms of innate and adaptive immunity.

Books on immunology and immunobiology (e.g. ASSIM books, Janis Kuby, Ivan Roitt, David Male, Charles Janeway). Recent and old scientific articles, to explain the fundamentals and the scientific advances.

Février - Mars.

EVRY

Olga Soutourina (PU UPSay) Ombeline Rossier (MCU UPSay) Johann Peltier (MCU UPSay).

Conferences: 10 hours Tutorial classes; Supervision/project tutoring 10 hours Personal work: at least 10 hours Oral examination and report.

The purpose of this teaching unit is to propose to students to explore a scientific question in Microbiology in an integrated way, both in terms of scale of analysis (from the molecule to the ecosystem) and methodologies or applications.
The students will carry out a personal project framed around a given aspect that they have chosen and that will be part of a general theme common to the whole class. Thus, collectively, the multiple facets of a current issue around an infectious agent will be taken into consideration, from the physiology and pathogenesis of the agent, to the interactions it maintains with the microbial communities and/or the host, to the practical implications of this knowledge in health or biotechnology. For example, Clostridium difficile infection may be a topic that can generate personal projects based on microbial interactions within intestinal microbiota (dysbiosis, bacteriophages), epidemiology (hypervirulent strains, recurrent infections) and therapeutic strategies. In connection with the problem addressed, students will be trained to use metagenomic data to compare the composition of the microbiota under standard conditions or following disturbances induced by antibiotic treatments and pathogen development.

Knowledge base in General Microbiology, Genetics, Molecular and Cell Biology, Biochemistry Open for Paris-Saclay International track.

Scientific papers and books in the field of Microbiology, documents on eCampus platform.

Février - Mars - Avril.

ORSAY - GIF-SUR-YVETTE

Catherine Berrier, PU Micaela Galante, MCU Sabir Jacquir, PU.

Cette UE de 25h est composée de 18h de cours et de 7h de travaux dirigés. Les séances de travaux dirigés sont vouées à résoudre des exercices basés sur des extraits de publications scientifiques et à l'analyse d'articles.

OAV1. Mettre en relation structure et fonctionnement des canaux ioniques
-Maitriser les concepts de base d'électrochimie et d'électrophysiologie nécessaires à la compréhension des propriétés électriques des membranaires.
-Expliquer les principes et les méthodes d'étude électrophysiologique des canaux ioniques.
-Relier les paramètres étudiés en électrophysiologie au mode d'action moléculaire des canaux ioniques.
OAV2. Décrire les principes de la communication intercellulaire dans le système nerveux et schématiser les étapes qui portent à la libération des neurotransmetteurs.
-Maîtriser les concepts fondamentaux de la Neuropharmacologie Moléculaire (affinité, activité et efficacité d'un médicament, courbe dose-effet, caractéristique liaison-effet, ..).
-Décrire les mécanismes de libération de neurotransmetteurs (transmission cholinergique).
OAV3. Décrire et schématiser les caractéristiques des récepteurs ionotropiques du glutamate et comparer leurs rôles à la synapse.
-Décrire la structure et caractériser les propriétés électrophysiologiques/pharmacologiques des récepteurs de type AMPA et NMDA.
-Décrire la coopération entre ces deux types de récepteurs à la synapse et leur implication dans la plasticité synaptique à long terme.

Architecture fonctionnelle et anatomique du neurone, structure de la membrane plasmique.

Physiologie du neurone, Tritsch-Chesnoy-Marchais-Felz, Ed. Doin. Biochimie et Biophysique des membranes, E. Shechter, Ed. Dunod. Cellular and Molecular Neuropharmacology, C. Hammond, Ed. Academic Press. From Molecules to networks, an introduction to Cellular and Molecular, J. H. Byrne-J. L. Roberts, Ed. Academic Press. Neurosciences, M. F. Bear-B. W. Connors-A. Paradiso, Ed. Pradel. Synapses, T. C. Südhof-C. F. Stevens, Ed. W. Maxwell CowanHoward Hughes Medical Institute.

Décembre.

ORSAY

Micaela Galante (UPSay) Emmanuel Culetto (UPSay) Valérie Enderline (UPSay) Jean-René Martin (CNRS) Sylvie Granon (UPSay) Daniel Shultz (CNRS) Isabelle Ferezou (CNRS) Heather McLean (UPSay).

L’UE est composée de cours magistraux (40h) et de travaux dirigés (10h) dispensés par des intervenants (enseignants-chercheurs et chercheurs). Les travaux dirigés sont essentiellement consacrés à l’analyse et la présentation des articles scientifiques illustrant des thèmes traités en cours. Les séances se dérouleront sous forme de présentation classique des articles ou sous forme de table ronde (travail de mise en débat de l’analyse par groupe avant une restitution collective). Un objectif majeur de ces séances est de raffiner les savoir-faire relatifs à la communication à travers des discussions collectives. Les cours magistraux et les travaux dirigés seront dispensés en français ou en anglais.

OAV1
Décrire et formaliser les fondements de la perception sensorielle
Mobiliser et restituer des connaissances sur la transduction, l’intégration et le codage de stimuli sensoriels (auditif, somesthésique, olfactif et visuel) par le système nerveux (modèles vertébrés et non-vertébrés)

OAV2
Enumérer le rôle de différents réseaux neuronaux à la base de divers comportements intégratifs
Analyser et interpréter des données expérimentales pour démontrer le rôle de certaines structures dans l’activité locomotrice et l’apprentissage moteur (cervelet)

OAV3
Illustrer et restituer des connaissances sur des mécanismes neurobiologiques, neurochimiques, cellulaires et moléculaires fondamentaux de la mémoire et la prise de décision dans des conditions normales et pathologiques

OAV4
Evaluer, critiquer et valoriser des arguments scientifiques représentant les avancées les plus récentes dans les domaines de recherche traités en cours
En s’appuyant sur les enseignements dispensés, l’étudiant sera capable d’interpréter, d’analyser et d’argumenter des articles scientifiques, afin de pouvoir animer une discussion scientifique, tout en gardant un esprit à la fois ouvert et critique.

Connaissances de neurobiologie cellulaire et de neuroanatomie fonctionnelle niveau licence 3ième année (voir bibliographie).

Les étudiants en Master 1 doivent avoir acquis en amont des connaissances basiques du système nerveux. Pour aider à la consolidation des connaissances, les livres suivants peuvent être utiles : Les bases de neurobiologie cellulaire : Physiologie du Neurone. Tritsch, Chesnoy-Marchais, Feltz. Editions Doin Les bases des systèmes sensoriels : Neurosciences : A la découverte du cerveau. Bear, Connors, Paradiso. Editions Pradel

Les articles de revue, publiés dans des journaux scientifiques réputés (et en langue anglaise) peuvent être mis à la disposition des étudiants.

Février - Mars - Avril.

ORSAY

Matthieu Jules (AgroParisTech, Micalis), Vincent Fromion (INRA, MaIAGE), Anne Goelzer (INRA, MaIAGE), Vincent Sauveplane (AgroParisTech, Micalis), Laurent Tournier (INRA, MaIAGE).

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological tools.

Global analyses (omics) currently generate large datasets that do not capture the complexity of living systems. Systems Biology is an approach where omics data are integrated and exploited (compared) through mathematical models of biological systems or sub-systems. The complexity of biological systems and the diversity of issues to be considered require the use of different types of modelling.
In this course, students will explore a number of mathematical approaches to tackle biological issues through the integration of "omics" data. The mathematical approaches include the methods known as constraint-based modeling, i.e. flux balance analysis, resource balance analysis, but also tools specific to the analysis of dynamic systems and Boolean systems.
On completion of the course students will be able to :
•understand and explain the challenges of using constraint-based modeling approaches to describe cellular behaviors
•summarize and present a scientific paper in the field.

The ability to use Matlab will be an asset but is not a prerequisite.

Recent and past scientific articles, to explain the fundamentals and scientific advances in systems biology. Two general references on these approaches : Systems Biology [Textbook], E. Klipp et al, Wiley-Blackwell, 2011. Metabolic engineering in the post genomic era, ed. B.N. Kholodenko, H.V. Westerhoff, Taylor & Francis, 2004.

Décembre.

JOUY-EN-JOSAS

Matthieu Jules Vincent Sauveplane Wolfram Liebermeister.

The course module is organized in 15h of lectures and 10h of tutorials to introduce knowledge and methodological tools.

In recent years the dynamics of biological systems has been increasingly described using concepts and terminology borrowed from economics: cells face trade-offs between different strategies for survival; metabolism can be viewed as a resource allocation problem; biomolecules can be associated with a 'value' within the free energy 'market' of the cell, etc. These concepts indicate the emergence of a new way of thinking about problems in biology.
In this course, we will explore biological questions that can be addressed using concepts of resource allocation, efficiency and optimality on (1) genome-scale cellular metabolism, (2) gene expression and protein synthesis, (3) cellular fitness and (4) game theory in cellular and multicellular biology.
At the end of the course, students will be able to:
•Explain the principles of cellular economics and resource allocation in living systems
•Analyse simple growth strategies of living systems in a competitive environment
•Describe simple models and identify their advantages and limitations.

Several first semester optional modules are highly recommended: Systems Biology I Systems Biology II.

Recent and past scientific articles, to explain the fundamentals and scientific advances in game theory, cellular resource allocation, cellular fitness, growth strategies etc. For instance, relevant publications are: •Shifts in growth strategies reflect tradeoffs in cellular economics. Molenaar D, van Berlo R, de Ridder D, Teusink B. ; Mol Syst Biol. 2009 •Mechanistic links between cellular trade-offs, gene expression, and growth. Weiße AY, Oyarzún DA, Danos V, Swain PS. ; Proc Natl Acad Sci U S A. 2015 •Plant height and evolutionary games. DS Falster and M Westoby; TRENDS in Ecology and

Décembre - Janvier.

JOUY-EN-JOSAS

Ioana Popescu Matthieu Jules Cécile Gasse.

The course module is organized in 16h of lectures and 9h of tutorials to introduce knowledge and methodological tools.

The aim of this module is to give students perspectives in Synthetic Biology, a field where novel biological and biologically based parts, devices and systems are (re)designed and constructed to perform new functions that do not exist in nature.
At the end of the course, students will be able to:
- Explain the strategies employed in the field of metabolic engineering for the production of sustainable biobased compounds
- Analyse simple synthetic regulatory circuits
- Explain the principles of genome engineering techniques and illustrate the synthetic genomics approaches
- Describe several orthogonal systems and analyse their advantages and limitations
Thus, students will have a strategic vision on how to progress in the field of synthetic biology: from the extraction of innovative knowledge from the available biological data to the transformation of the data into new rational and useful knowledge.

Several first semester optional modules are highly recommended: Systems Biology I Systems Biology II Cellular Economics.

Paul S Freemont (Editor) and Richard I Kitney (Editor). Synthetic Biology: A Primer. Imperial College Press, 2012. Daniel G. Gibson (Editor), Clyde A. Hutchison (III) (Editor), Hamilton Othanel Smith (Editor) and J. Craig Venter (Editor). Synthetic Biology: Tools for Engineering Biological Systems. Cold Spring Harbor Laboratory Press, 2017. Christina Smolke (Editor), Sang Yup Lee (Series Editor), Jens Nielsen (Series Editor) and Gregory Stephanopoulos (Series Editor). Synthetic Biology: Parts, Devices and Applications. Wiley-Blackwell, 2018.

Février - Mars - Avril.

EVRY

Morgane Locker Odile Bronchain Emmanuel Culetto Christophe Lefebvre Anne-Marie Pret Isabelle Guénal Marianne Malartre François Agnès.

One week in a lab from Paris-Saclay.

Working on multicellular whole organisms is often hard to realize in the environment of a classical Lab course. This workshop, in the context of a research lab on campus, is meant to allow you to address biological issues in adults or embryos, in a normal or pathological context, using the specific approaches that apply to xenopus, zebrafish, nematode, mouse, drosophila, podospora and arabidopsis.
This course will allow you to get more familiar with sophisticated imaging approaches (3D imaging, confocal microscopy, time lapse,...), as well as genetics and DNA/RNA tools that allow tissue/cell specific and temporal modulation of gene expression.
This 2,5 ECTS version is a one-week internship.

None.

References will be sent by the tutor, depending on the subject/lab.

Novembre - Décembre - Janvier.

ORSAY - GIF-SUR-YVETTE - MONTIGNY-LE-BRETONNEUX

Responsables Université Paris-Saclay : Marie-Hélène Cuif, marie-helene.cuif@universite-paris-saclay.fr Sébastien Bloyer, sebastien.bloyer@universite-paris-saclay.fr Odile Bronchain, odile.bronchain@universite-paris-saclay.fr Cécile Lagaudrière, cecile.lagaudriere-gesbert@universite-paris-saclay.fr Sylvain Fisson, sylvain.fisson@univ-evry.fr.

During the first semester, the students have to find a host laboratory. To this end they must write a CV, consult the internship offers and contact research teams of their choice for an interview. The internship is tied up to the 'Scientific project' teaching unit, during which the scientific context and the experimental approaches suitable to address the biological questions will be defined. The internship spans 8-weeks in an academic laboratory or in a R&D department within a company, in France or abroad. At the end of the internship, the students complete a research report and an oral presentation, to highlight the biological questions raised, the experimental designs and to present and discuss their results.

The internship allows students to get familiar with various experimental approaches as well as the daily activities of a research team.
During the internship, the students participate in an ongoing research project under the guidance of laboratory staff scientists or engineers. They attend lab meetings and conferences. They are introduced to the hygiene and safety rules. They acquire and analyze experimental data. They have to synthetize their results in the form of a written report and an oral defense.
At the end of this teaching unit, the student will be able to:
- apply to research teams
- integrate a research team and participate in its activities
- follow Health and Safety rules
- to carry out a scientific experiment and integrate the controls required for its interpretation.
- write a laboratory notebook
- analyze critically the results obtained
- synthesize and present a scientific research process and the results obtained in oral and written form.

None.

Avril - Mai - Juin.

SCEAUX - ORSAY - GUYANCOURT - EVRY - GIF-SUR-YVETTE - CHATENAY - VERSAILLES - PARIS - KREMLIN-BICETRE - ST-QUENTIN-EN-YVELINES - PALAISEAU - MONTIGNY-LE-BRETONNEUX - COURCOURONNES - BURES-SUR-YVETTE - JOUY-EN-JOSAS

Responsables Université Paris-Saclay : Marie-Hélène Cuif, marie-helene.cuif@universite-paris-saclay.fr Sébastien Bloyer, sebastien.bloyer@universite-paris-saclay.fr Odile Bronchain, odile.bronchain@universite-paris-saclay.fr Cécile Lagaudrière, cecile.lagaudriere-gesbert@universite-paris-saclay.fr Sylvain Fisson, sylvain.fisson@univ-evry.fr Frédéric Crémazy, frederic.cremazy@uvsq.fr.

The Scientific Project is organized over a period of 8 weeks at a rate of one day per week spent in the host laboratory. This period is devoted to discussions between the student and his supervisor, the reflection and a bibliographic work to define the internship project. The student will present a bibliographic synthesis of the topic and the problematic of his internship project in a written report.

The Scientific Project is a groundwork for the laboratory internship. It consists of a thoughtful work based on bibliographic researches and on discussions with the internship's supervisor.
It aims at clarifying the general scientific context and the state of knowledge. It allows highlighting the scientific questions that will be addressed during the internship, the experimental models chosen and the workflow of experiences that will be conducted. The whole is synthesized in a written report.
At the end of this training, the student will be able to:
- define a biological problem
- acquire, analyze and synthesize data from the literature
- formulate scientific hypotheses
- build a coherent scientific approach
- write a research project.

None.

None.

Février - Mars - Avril.

Odile Bronchain: odile.bronchain@universite-paris-saclay.fr.

Ludwig-Maximilian University Munich (Germany), Lund University (Sweden), University of Porto (Portugal), University of Szeged (Hungary) and Université Paris-Saclay have joined forces to create a pilot European University, driven by European values and committed to higher education and training on challenges related to global health and well-being.
Within EUGLOH, the five universities share the ambition to combine their expertise and resources to offer the best education and training to their students and thereby become a world-class higher education alliance, based on the excellence of their teaching and cutting-edge research and equipment.
EUGLOH’s visions and objectives are:
• Training the future generations of European innovators, practitioners, experts and leaders serving all sectors of the society, ready to face interdisciplinary societal challenges related to Global Health
• Becoming a world-class higher education alliance focused on Global Health and well-being challenges
• Promoting European values, such as solidarity, equality of opportunities, inclusiveness, respect for human rights and full access to welfare
• Setting the foundation of a common European health area
• Building a European campus with a high level of integration sustained by joint procedures and structures
• Boosting attractiveness and competitiveness of European higher education, research and innovation
ALLIANCE FOR GLOBAL HEALTH: https://www.eugloh.eu/about/vision-and-objectives/plaquette-EUGLOH-EN-page-par-page%20(1)%20(1).pdf.

This optional teaching unit is subjected to registration fees. Please consult the dedicated web site for more information:
https://www.sciences.universite-paris-saclay.fr/french-foreign-language

Contact: contact-fle.langues@universite-paris-saclay.fr.

Csilla Ducrocq : csilla.ducrocq@universite-paris-saclay.fr.

This course aims at raising intercultural awareness and learning to communicate across cultures through exploring the visible and hidden aspects of culture, cultural similarities and differences in the participating student groups from 3 European universities: U. Paris-Saclay (France), U. Szeged (Hungary), U. Ludwig Maximilian (Germany). The main objective of such intercultural exchanges is not necessarily to make a list of the components of a specific culture, but to encourage an enquiring questioning attitude in order to promote tolerance, acceptance and respect for cultural diversity, to provide students with skills that will enable them to cooperate across cultures. Such skills have become essential in today’s globalized world. Participating students will receive a certificate of Intercultural awareness according to the Common European Framework of Reference for Languages.
The course consists of 20 hrs of theoretical background courses and 6 hours of online interaction in smaller groups with students from the 3 participating universities.

None.

September to November.

Odile Bronchain: odile.bronchain@universite-paris-saclay.fr Laurent Théodore: laurent.theodore@universite-prais-saclay.fr.

The optional internship can take place at any time during the year (From September to August) in an academic laboratory or in a R&D department within a company, in France or abroad provided that the internship does not interfere with the academic schedule. The duration of the internship is to be established between the student and his tutor, and is subjected to an official Internship Agreement.

Optional internships allow students to gain experience in new fields and professional activities and refine their final goals and career plans.
An internship allows students to get familiar with various experimental approaches as well as the daily activities of a research team.
During the internship, the students participate in an ongoing research project under the guidance of laboratory staff scientists or engineers. They attend lab meetings and conferences. They are introduced to the hygiene and safety rules. They acquire and analyze experimental data. They have to synthetize their results in the form of a written report and an oral defense.
At the end of this teaching unit, the student will be able to:
- apply to research teams
- integrate a research team and participate in its activities
- follow Health and Safety rules
- to carry out a scientific experiment and integrate the controls required for its interpretation.
- write a laboratory notebook
- analyze critically the results obtained
- synthesize and present a scientific research process and the results obtained in oral and written form.

None.

None.

From September to August.